compute_velocity_on_grid: Compute velocity on grid The original python code is on...

In zh542370159/SCP: Single Cell Pipeline

Compute velocity on grid The original python code is on https://github.com/theislab/scvelo/blob/master/scvelo/plotting/velocity_embedding_grid.py

Description

Compute velocity on grid The original python code is on https://github.com/theislab/scvelo/blob/master/scvelo/plotting/velocity_embedding_grid.py

Usage

compute_velocity_on_grid(
  X_emb,
  V_emb,
  density = NULL,
  smooth = NULL,
  n_neighbors = NULL,
  min_mass = NULL,
  scale = 1,
  adjust_for_stream = FALSE,
  cutoff_perc = NULL
)

Arguments

X_emb	A matrix of dimension n_obs x n_dim specifying the embedding coordinates of the cells.
V_emb	A matrix of dimension n_obs x n_dim specifying the velocity vectors of the cells.
density	An optional numeric value specifying the density of the grid points along each dimension. Default is 1.
smooth	An optional numeric value specifying the smoothing factor for the velocity vectors. Default is 0.5.
n_neighbors	An optional numeric value specifying the number of nearest neighbors for each grid point. Default is ceiling(n_obs / 50).
min_mass	An optional numeric value specifying the minimum mass required for a grid point to be considered. Default is 1.
scale	An optional numeric value specifying the scaling factor for the velocity vectors. Default is 1.
adjust_for_stream	A logical value indicating whether to adjust the velocity vectors for streamlines. Default is FALSE.
cutoff_perc	An optional numeric value specifying the percentile cutoff for removing low-density grid points. Default is 5.

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.